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Background: Sweet potato ( Ipomoea batatas (L.) Lam.), a key global root crop, faces challenges due to its narrow genetic background. This issue can be addressed by utilizing the diverse genetic resources of sweet potato's wild relatives, which are invaluable for its genetic improvement. Methods: The morphological differences in leaves, stems, and roots among 13 Ipomoea species were observed and compared. Chromosome numbers were determined by examining metaphase cells from root tips. Fluorescence in situ hybridization (FISH) was used to identify the number of 5S and 18S rDNA sites in these species. PCR amplification was performed for both 5S and 18S rDNA, and phylogenetic relationships among the species were analyzed based on the sequences of 18S rDNA. Results: Three species were found to have enlarged roots among the 13 Ipomoea species. Chromosome analysis revealed that I. batatas had 90 chromosomes, Ipomoea pes-tigridis had 28 chromosomes, while the remaining species possessed 30 chromosomes. Detection of rDNA sites in the 13 species showed two distinct 5S rDNA site patterns and six 18S rDNA site patterns in the 12 diploid species. These rDNA sites occurred in pairs, except for the seven 18S rDNA sites observed in Ipomoea digitata . PCR amplification of 5S rDNA identified four distinct patterns, while 18S rDNA showed only a single pattern across the species. Phylogenetic analysis divided the 13 species into two primary clades, with the closest relationships found between I. batatas and Ipomoea trifida , as well as between Ipomoea platensis and I. digitata . Conclusions: These results enhance our understanding of the diversity among Ipomoea species and provide valuable insights for breeders using these species to generate improved varieties.

Growth-regulating factor (GRF) is a multi-gene family that plays an important role in plant growth and development and is widely present in plants. Currently, GRF gene members have been reported in many plants, but the GRF gene family has not been found in sweet potato. In this study, ten GRF genes were identified in sweet potato ( Ipomoea batatas ), twelve and twelve were identified in its two diploid relatives ( Ipomoea trifida ) and ( Ipomoea triloba ), which were unevenly distributed on nine different chromosomes. Subcellular localization analysis showed that GRF genes of sweet potato, I. trifida , and I. triloba were all located in the nucleus. The expression analysis showed that the expression of IbGRFs was diverse in different sweet potato parts, and most of the genes were upregulated and even had the highest expression in the vigorous growth buds. These findings provide molecular characterization of sweet potato and its two diploid relatives, the GRF families, further supporting functional characterization.

Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1-5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown yet fundamental to the community assembly of host-associated microbiomes, with implications for the eco-evolutionary dynamics of microbes and hosts. Using Ipomoea hederacea , ivyleaf morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect Mendelian locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.IMPORTANCEWe investigated how host genetic variation affects the assembly of Ipomoea hederacea 's natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance and community composition., Competing Interests: The authors declare no conflict of interest.

Ipomoea species have diverse uses as ornamentals, food, and medicine. However, their genomic information is limited; I. alba and I. obscura were sequenced and assembled. Their chloroplast genomes were 161,353 bp and 159,691 bp, respectively. Both genomes exhibited a quadripartite structure, consisting of a pair of inverted repeat (IR) regions, which are separated by the large single-copy (LSC) and small single-copy (SSC) regions. The overall GC content was 37.5% for both genomes. A total of 104 and 93 simple sequence repeats, 50 large repeats, and 30 and 22 short tandem repeats were identified in the two chloroplast genomes, respectively. G and T were more preferred than C and A at the third base position based on the Parity Rule 2 plot analysis, and the neutrality plot revealed correlation coefficients of 0.126 and 0.105, indicating the influence of natural selection in shaping the codon usage bias in most protein-coding genes (CDS). Genome comparative analyses using 31 selected Ipomoea taxa from Thailand showed that their chloroplast genomes are rather conserved, but the presence of expansion or contraction of the IR region was identified in some of these Ipomoea taxa. A total of five highly divergent regions were identified, including the CDS genes accD, ndhA, and ndhF, as well as the intergenic spacer regions psbI-atpA and rpl32-ccsA. Phylogenetic analysis based on both the complete chloroplast genome sequence and CDS datasets of 31 Ipomoea taxa showed that I. alba is resolved as a group member for series (ser.) Quamoclit, which contains seven other taxa, including I. hederacea, I. imperati, I. indica, I. nil, I. purpurea, I. quamoclit, and I. × sloteri, while I. obscura is grouped with I. tiliifolia, both of which are under ser. Obscura, and is closely related to I. biflora of ser. Pes-tigridis. Divergence time estimation using the complete chloroplast genome sequence dataset indicated that the mean age of the divergence for Ipomoeeae, Argyreiinae, and Astripomoeinae, was approximately 29.99 Mya, 19.81 Mya, and 13.40 Mya, respectively. The node indicating the divergence of I. alba from the other members of Ipomoea was around 10.06 Mya, and the split between I. obscura and I. tiliifolia is thought to have happened around 17.13 Mya. The split between the I. obscura accessions from Thailand and Taiwan is thought to have taken place around 0.86 Mya., (© 2024. The Author(s).)

So far, the physiological and molecular mechanisms of the impact of arbuscular mycorrhizal fungus (AMF) on Cd absorption, transport and detoxification in Ipomoea aquatica (water spinach) are still unclear. In the present study, a pot experiment was performed to investigate the impact of AMF-Glomus versiforme (Gv) on the photosynthetic characteristics, Cd uptake, antioxidative system and transcriptome in water spinach in the soils supplemented with 5 mg Cd kg -1 . Gv inoculation improved significantly the photosynthetic characteristics and growth of water spinach. Furthermore, Gv colonization significantly promoted the activities of catalase (CAT), peroxidase (POD) and glutathione reductase (GR), contents of glutathione (GSH) and ascorbic acid (AsA), and the total antioxidant capacity (TCA), but decreased malondialdehyde (MDA) content in water spinach. In addition, Gv inoculation significantly increased pH in rhizosphere soils and decreased the Cd concentrations and uptakes in water spinach. Importantly, 2670 differentially expressed genes (DEGs) were screened in water spinach root colonized with Gv in 5 mg Cd kg -1 soil, of which 2008 DEGs were upregulated and 662 DEGs were downregulated. Especially, the expression levels of POD, CAT, GR, dehydroascorbate reductase 2 (DHAR2), glutathione S-transferase U8 (GSTU8) and glutathione synthetase (GSHS) and cytochrome P450 (Cyt P450) genes were significantly up-regulated in water spinach inoculated with Gv. Meanwhile, the plant cadmium resistance protein 2 (PCR2), metal tolerance protein 4 (MTP4), ATP-binding cassette transporter C family member (ABCC), ABC-yeast cadmium factor 1 (ABC-YCF1) and metallothionein (MT) genes were also up-regulated in mycorrhizal water spinach. Our results firstly elucidated the mechanism by which AMF reduced the uptake and phytotoxicity of Cd in water spinach through a transcriptome analysis., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The starch synthase (SS) plays important roles in regulating plant growth and development and responding to adversity stresses. Although the SS family has been studied in many crops, it has not been fully identified in sweet potato and its two related species. In the present study, eight SSs were identified from Ipomoea batatas ( I. batata ), Ipomoea trifida ( I. trifida ), and Ipomoea trlioba ( I. trlioba ), respectively. According to the phylogenetic relationships, they were divided into five subgroups. The protein properties, chromosomal location, phylogenetic relationships, gene structure, cis-elements in the promoter, and interaction network of these proteins were also analyzed; stress expression patterns were systematically analyzed; and real-time polymerase chain reaction (qRT-PCR) analysis was performed. Ipomoea batatas starch synthase ( IbSSs ) were highly expressed in tuber roots, especially Ipomoea batatas starch synthase 1 ( IbSS1 ) and Ipomoea batatas starch synthase 6 ( IbSS6 ), which may play an important role in root development and starch biosynthesis. At the same time, the SS genes respond to potassium deficiency, hormones, cold, heat, salt, and drought stress. This study offers fresh perspectives for enhancing knowledge about the roles of SSs and potential genes to enhance productivity, starch levels, and resistance to environmental stresses in sweet potatoes.

The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida., (© 2024. The Author(s).)

The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering time in water spinach, we performed transcriptome sequencing on water spinach under long- and short-day conditions with eight time points. Our results indicated that there were 6615 circadian-rhythm-related genes under the long-day condition and 8691 under the short-day condition. The three key circadian-rhythm genes, IaCCA1 , IaLHY , and IaTOC1 , still maintained single copies and similar IaCCA1 , IaLHY , and IaTOC1 feedback expression patterns, indicating the conservation of reverse feedback. In the photoperiod pathway, highly conserved GI genes were amplified into two copies ( IaGI1 and IaGI2 ) in water spinach. The significant difference in the expression of the two genes indicates functional diversity. Although the photoperiod core gene FT was duplicated to three copies in water spinach, only IaFT1 was highly expressed and strongly responsive to the photoperiod and circadian rhythms, and the almost complete inhibition of IaFT1 in water spinach may be the reason why water spinach does not bloom, no matter how long it lasts under the long-day condition. Differing from other species ( I. nil , I. triloba, I. trifida ) of the Ipomoea genus that have three CO members, water spinach lacks one of them, and the other two CO genes ( IaCO1 and IaCO2 ) encode only one CCT domain. In addition, through weighted correlation network analysis (WGCNA), some transcription factors closely related to the photoperiod pathway were obtained. This work provides valuable data for further in-depth analyses of the molecular regulation of the flowering time in water spinach and the Ipomoea genus.

Malate dehydrogenase (MDH; EC 1.1.1.37) plays a vital role in plant growth and development as well as abiotic stress responses, and it is widely present in plants. However, the MDH family genes have not been explored in sweet potato. In this study, nine, ten, and ten MDH genes in sweet potato ( Ipomoea batatas ) and its two diploid wild relatives, Ipomoea trifida and Ipomoea triloba , respectively, were identified. These MDH genes were unevenly distributed on seven different chromosomes among the three species. The gene duplications and nucleotide substitution analysis (Ka/Ks) revealed that the MDH genes went through segmental duplications during their evolution under purifying selection. A phylogenetic and conserved structure divided these MDH genes into five subgroups. An expression analysis indicated that the MDH genes were omni-presently expressed in distinct tissues and responded to various abiotic stresses. A transcription factor prediction analysis proved that Dof, MADS-box, and MYB were the main transcription factors of sweet potato MDH genes. These findings provide molecular features of the MDH family in sweet potato and its two diploid wild relatives, which further supports functional characterizations.

How do selection and standing genetic variation shape population divergence across landscapes? Henry and Stinchcombe estimated selection gradients on traits in the ivy-leaved morning glory (Ipomoea hederacea) in the field and compared them with the G-matrix and population divergence for four populations in North America. The authors show that population divergence and genetic covariances are largely unaligned with the selection gradient at the species' range edge. These findings raise the question of whether limited evolvability or multivariate genetic variation of populations at range edges prevent species from range expansion, which is important for understanding the role of genetic constraint in population divergence and predicting local adaptation in the face of climate change., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Abscisic acid (ABA), a critical phytohormone that regulates plant development and stress response, is sensed by the ABA receptors PYR/PYL/RCAR (PYLs). The PYL genes have been widely studied in multiple plant species, while a systematic analysis of PYL genes in the genus Ipomoea remains unperformed. Here, a total of 13, 14, and 14 PYLs were identified in Ipomoea batatas , Ipomoea trifida , and Ipomoea triloba , respectively. Fragment duplication was speculated to play prominent roles in Ipomoea PYL gene expansions. These Ipomoea PYLs were classified into three subfamilies via phylogenetic analysis, which was supported by exon-intron structures and conserved motif analyses. Additionally, the interspecies collinearity analysis further depicted a potential evolutionary relationship between them. Moreover, qRT-PCR analysis showed that multiple IbPYLs are highly and differentially responsive to abiotic stress treatments, suggesting their potential roles in sweetpotato stress responses. Taken together, these data provide valuable insights into the PYLs in the genus Ipomoea , which may be useful for their further functional analysis of their defense against environmental changes.

ACTINs are structural proteins widely distributed in plants. They are the main components of microfilaments and participate in many crucial physiological activities, including the maintenance of cell shape and cytoplasmic streaming. Meanwhile, ACTIN , as a housekeeping gene, is widely used in qRT-PCR analyses of plants. However, ACTIN family genes have not been explored in the sweet potato. In this study, we identified 30, 39, and 44 ACTINs in the cultivated hexaploid sweet potato ( Ipomoea batatas , 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively, via analysis of their genome structure and by phylogenetic characterization. These ACTINs were divided into six subgroups according to their phylogenetic relationships with Arabidopsis thaliana . The physiological properties of the protein, chromosome localization, phylogenetic relationship, gene structure, promoter cis -elements, protein interaction networks, and expression patterns of these 113 ACTINs were systematically investigated. The results suggested that homologous ACTINs are differentiated in the sweet potato and its two diploid relatives, and play various vital roles in plant growth, tuberous root development, hormone crosstalk, and abiotic stress responses. Some stable ACTINs that could be used as internal reference genes were found in the sweet potato and its two diploid relatives, e.g., IbACTIN18 , -20 , and -16.2 ; ItfACTIN2.2 , -16 , and -10 ; ItbACTIN18 and -19.1 . This work provides a comprehensive comparison and furthers our understanding of the ACTIN genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potatoes.

Reproductive isolation between selfing and outcrossing species can arise through diverse mechanisms, some of which are directly associated with differences in mating system. We dissected cross-incompatibility between the highly selfing morning glory Ipomoea lacunosa and its mixed-mating sister species Ipomoea cordatotriloba. We found that cross-incompatibility is complex, with contributions acting both before and after fertilization. We then investigated whether the transition in mating system may have facilitated the evolution of these reproductive barrier components through mismatched floral morphology, differences in reproductive context, or both. We found evidence that morphological mismatch likely contributes to reproductive isolation in at least one cross-direction and that other pollen-pistil interactions are present. We also identified hybrid seed inviability consistent with the predictions of the weak-inbreeder, strong-outbreeder hypotheses, suggesting endosperm misregulation plays an important role in cross-incompatibility. In contrast, we did not find evidence consistent with the prezygotic weak-inbreeder, strong-outbreeder hypothesis. Our study highlights the complexity of reproductive isolation between outcrossing and selfing species and the extent to which evolutionary consequences of mating system transitions can facilitate speciation., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE).)

The multivariate evolution of populations is the result of the interactions between natural selection, drift, and the underlying genetic structure of the traits involved. Covariances among traits bias responses to selection, and the multivariate axis which describes the greatest genetic variation is expected to be aligned with patterns of divergence across populations. An exception to this expectation is when selection acts on trait combinations lacking genetic variance, which limits evolutionary change. Here we used a common garden field experiment of individuals from 57 populations of Ipomoea hederacea to characterize linear and nonlinear selection on 5 quantitative traits in the field. We then formally compare patterns of selection to previous estimates of within population genetic covariance structure (the G-matrix) and population divergence in these traits. We found that selection is poorly aligned with previous estimates of genetic covariance structure and population divergence. In addition, the trait combinations favored by selection were generally lacking genetic variation, possessing approximately 15%-30% as much genetic variation as the most variable combination of traits. Our results suggest that patterns of population divergence are likely the result of the interplay between adaptive responses, correlated responses, and selection favoring traits lacking genetic variation., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking., (© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.)

Heritable fungal endosymbiosis is underinvestigated in plant biology and documented in only three plant families (Convolvulaceae, Fabaceae, and Poaceae). An estimated 40% of morning glory species in the tribe Ipomoeeae (Convolvulaceae) have associations with one of two distinct heritable, endosymbiotic fungi (Periglandula and Chaetothyriales) that produce the bioactive metabolites ergot alkaloids, indole diterpene alkaloids, and swainsonine, which have been of interest for their toxic effects on animals and potential medical applications. Here, we report the occurrence of ergot alkaloids, indole diterpene alkaloids, and swainsonine in the Convolvulaceae; and the fungi that produce them based on synthesis of previous studies and new indole diterpene alkaloid data from 27 additional species in a phylogenetic, geographic, and life-history context. We find that individual morning glory species host no more than one metabolite-producing fungal endosymbiont (with one possible exception), possibly due to costs to the host and overlapping functions of the alkaloids. The symbiotic morning glory lineages occur in distinct phylogenetic clades, and host species have significantly larger seed size than nonsymbiotic species. The distinct and widely distributed endosymbiotic relationships in the morning glory family and their alkaloids provide an accessible study system for understanding heritable plant-fungal symbiosis evolution and their potential functions for host plants., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Background: Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available., Results: This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I-VII), and the members in the same group exhibited similar exon-intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis., Conclusions: Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes., (© 2023. The Author(s).)

The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. Ipomoea aquatica is one of the most important nutrient-rich vegetables. Compared to the common green-stemmed I. aquatica , purple-stemmed I. aquatica has extremely high contents of anthocyanins. However, the information on bHLH genes in I. aquatica and their role in regulating anthocyanin accumulation is still unclear. In this study, we confirmed a total of 157 bHLH genes in the I. aquatica genome, which were classified into 23 subgroups according to their phylogenetic relationship with the bHLH of Arabidopsis thaliana (AtbHLH). Of these, 129 IabHLH genes were unevenly distributed across 15 chromosomes, while 28 IabHLH genes were spread on the scaffolds. Subcellular localization prediction revealed that most IabHLH proteins were localized in the nucleus, while some were in the chloroplast, extracellular space, and endomembrane system. Sequence analysis revealed conserved motif distribution and similar patterns of gene structure within IabHLH genes of the same subfamily. Analysis of gene duplication events indicated that DSD and WGD played a vital role in the IabHLH gene family expansion. Transcriptome analysis showed that the expression levels of 13 IabHLH genes were significantly different between the two varieties. Of these, the IabHLH027 had the highest expression fold change, and its expression level was dramatically higher in purple-stemmed I. aquatica than that in green-stemmed I. aquatica . All upregulated DEGs in purple-stemmed I. aquatica exhibited the same expression trends in both qRT-PCR and RNA-seq. Three downregulated genes including IabHLH142 , IabHLH057 , and IabHLH043 determined by RNA-seq had opposite expression trends of those detected by qRT-PCR. Analysis of the cis-acting elements in the promoter region of 13 differentially expressed genes indicated that light-responsive elements were the most, followed by phytohormone-responsive elements and stress-responsive elements, while plant growth and development-responsive elements were the least. Taken together, this work provides valuable clues for further exploring IabHLH function and facilitating the breeding of anthocyanin-rich functional varieties of I. aquatica .

Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato ( Ipomoea batatas ) and its two wild relatives, Ipomoea triloba , and Ipomoea trifida . Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H 2 O 2 , cold, heat, Fusarium oxysporum f. sp. batatas ( Fob ), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3 .1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.

Sugar Will Eventually be Exported Transporter (SWEET) proteins are key transporters in sugar transportation. They are involved in the regulation of plant growth and development, hormone crosstalk, and biotic and abiotic stress responses. However, SWEET family genes have not been explored in the sweet potato. In this study, we identified 27, 27, and 25 SWEETs in cultivated hexaploid sweet potato ( Ipomoea batatas , 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These SWEETs were divided into four subgroups according to their phylogenetic relationships with Arabidopsis . The protein physiological properties, chromosome localization, phylogenetic relationships, gene structures, promoter cis -elements, protein interaction networks, and expression patterns of these 79 SWEETs were systematically investigated. The results suggested that homologous SWEETs are differentiated in sweet potato and its two diploid relatives and play various vital roles in plant growth, tuberous root development, carotenoid accumulation, hormone crosstalk, and abiotic stress response. This work provides a comprehensive comparison and furthers our understanding of the SWEET genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potato.

Key Message: A novel interspecific somatic hybrid combining drought tolerance and high quality of sweet potato and Ipomoea triloba L. was obtained and its genetic and epigenetic variations were studied. Somatic hybridization can be used to overcome the cross-incompatibility between sweet potato (Ipomoea batatas (L.) Lam.) and its wild relatives and transfer useful and desirable genes from wild relatives to cultivated plants. However, most of the interspecific somatic hybrids obtained to date cannot produce storage roots and do not exhibit agronomic characters. In the present study, a novel interspecific somatic hybrid, named XT1, was obtained through protoplast fusion between sweet potato cv. Xushu 18 and its wild relative I. triloba. This somatic hybrid produced storage roots and exhibited significantly higher drought tolerance and quality compared with its cultivated parent Xushu 18. Transcriptome and real-time quantitative PCR (qRT-PCR) analyses revealed that the well-known drought stress-responsive genes in XT1 and I. triloba were significantly up-regulated under drought stress. The genomic structural reconstructions between the two genomes of the fusion parents in XT1 were confirmed using genomic in situ hybridization (GISH) and specific nuclear and cytoplasmic DNA markers. The DNA methylation variations were characterized by methylation-sensitive amplified polymorphism (MSAP). This study not only reveals the significance of somatic hybridization in the genetic improvement of sweet potato but also provides valuable materials and knowledge for further investigating the mechanism of storage root formation in sweet potato., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The anthocyanins are pigments responsible for a wide range of colours in plants, from blue, red and purple, play essential biological roles as well as their genes are evolutionarily conserved. Purple sweet potatoes have anthocyanins as the predominant colour, even though they are present in orange roots masked by carotenoids. Several studies have focused on molecular aspects of anthocyanin genes, mainly in wild Ipomoea species, although the structure and segregation analysis of those genes in sweet potato hexaploid species are still unknown. Based on an "exon-primed intron-crossing" (EPIC) approach, fourteen pairs of primers were designed, on five structural anthocyanin genes as candidates. The strategy exploits the Intron Length Polymorphism (ILP) from Candidate Genes (CG), resulting in 93% of successful markers giving scorable and reproducible alleles. The results allowed to define partial structure and sequence of the introns and exons from the selected CG, and to determine patterns of sequence variation. The evaluation of marker dosage and allelic segregations in an Ipomoea batatas (L.) Lam mapping population identified several alleles for linkage analysis. The study validated the utility of ILP-CG markers for genetic diversity and conservation applicability and a successful amplification gradient across wild Ipomoea species validated their transferability.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of of the Editors-in-Chief. A large part of the article is highly similar to the paper previously published by Wenqian Hou, Lei Ren, Yang Zhang, Haoyun Sun, Tianye Shi, Yulan Gu, Aimin Wang, Daifu Ma, Zongyun Li and Lei Zhang in Scientia Horticulturae 288 (2021) 110374 https://doi.org/10.1016/j.scienta.2021.110374. In particular, a large part of the two articles shows a study on the same gene family in the same plant, with similar methodological approaches, resulting in a series of highly similar figures. One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and has not appeared in a publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

Stress-associated protein (SAP) genes-encoding A20/AN1 zinc-finger domain-containing proteins-play pivotal roles in regulating stress responses, growth, and development in plants. They are considered suitable candidates to improve abiotic stress tolerance in plants. However, the SAP gene family in sweetpotato ( Ipomoea batatas ) and its relatives is yet to be investigated. In this study, 20 SAPs in sweetpotato, and 23 and 26 SAPs in its wild diploid relatives Ipomoea triloba and Ipomoea trifida were identified. The chromosome locations, gene structures, protein physiological properties, conserved domains, and phylogenetic relationships of these SAPs were analyzed systematically. Binding motif analysis of IbSAPs indicated that hormone and stress responsive cis -acting elements were distributed in their promoters. RT-qPCR or RNA-seq data revealed that the expression patterns of IbSAP , ItbSAP , and ItfSAP genes varied in different organs and responded to salinity, drought, or ABA (abscisic acid) treatments differently. Moreover, we found that IbSAP16 driven by the 35 S promoter conferred salinity tolerance in transgenic Arabidopsis . These results provided a genome-wide characterization of SAP genes in sweetpotato and its two relatives and suggested that IbSAP16 is involved in salinity stress responses. Our research laid the groundwork for studying SAP-mediated stress response mechanisms in sweetpotato.

Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical, and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by Pacific Biosciences HiFi and Hi-C sequencing, with the assembly size of 733.0 Mb, the contig N50 of 43.8 Mb, the scaffold N50 of 45.7 Mb, and the Benchmarking Universal Single-Copy Orthologs complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere to telomere. The transposable element content of Ipomoea cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the Benchmarking Universal Single-Copy Orthologs complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that Ipomoea cairica formed a clade with Ipomoea aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of Ipomoea cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

The sweet potato ( Ipomoea batatas (L.) Lam.) is an important and widely grown crop, and the nitrogenase reductase ( nifH ) gene is the most widely sequenced marker gene used to identify nitrogen-fixing bacteria and archaea. There have been many examples of the isolation of the diazotrophic endophytes in sweet potatoes, and there has been no report on whether sweet potatoes and their wild ancestors harbored nifH genes. In this study, a comprehensive analysis of nifH genes has been conducted on these species by using bioinformatics and molecular biology methods. A total of 20, 19 and 17 nifH genes were identified for the first time in sweet potatoes, I. trifida and I. triloba , respectively. Based on a phylogenetic analysis, all of the nifH genes, except for g10233.t1 , itf14g14040.t1 and itb14g15470.t1 , were clustered into five independent clades: I, II, III, IV and V. The nifH genes clustered in the same phylogenetic branch showed a more similar distribution of conserved motifs and exons-introns than those of the other ones. All of the identified genes were further mapped on the 15 chromosomes of the sweet potato, I. trifida and I. triloba . No segmental duplication was detected in each genome of three Ipomoea species, and 0, 8 and 7 tandemly duplicated gene pairs were detected in the genome of the sweet potato, I. trifida and I. triloba , respectively. Synteny analysis between the three Ipomoea species revealed that there were 7, 7 and 8 syntenic gene pairs of nifH genes detected between the sweet potato and I. trifida , between the sweet potato and I. triloba and between I. trifida and I. triloba , respectively. All of the duplicated and syntenic nifH genes were subjected to purifying selection inside duplicated genomic elements during speciation, except for the tandemly duplicated gene pair itf11g07340.t2_itf11g07340.t3 , which was subjected to positive selection. Different expression profiles were detected in the sweet potato, I. trifida and I. triloba . According to the above results, four nifH genes of the sweet potato ( g950 , g16683 , g27094 and g33987 ) were selected for quantitative real-time polymerase chain reaction (qRT-PCR) analysis in two sweet potato cultivars (Eshu 15 and Long 9) under nitrogen deficiency (N0) and normal (N1) conditions. All of them were upregulated in the N1 treatment and were consistent with the analysis of the RNA-seq data. We hope that these results will provide new insights into the nifH genes in the sweet potato and its wild ancestors and will contribute to the molecular breeding of sweet potatoes in the future.

Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in Ipomoea trifida , and little is known regarding storage root (SR) development. In this work, we identified a total of 37 expansins ( ItrEXPs ) in our previously reported SR-forming I. trifida strain Y22 genome, which included 23 ItrEXPAs , 4 ItrEXPBs , 2 ItrEXLAs and 8 ItrEXLBs . The phylogenetic relationship, genome localization, subcellular localization, gene and protein structure, promoter cis -regulating elements, and protein interaction network were systematically analyzed to reveal the possible roles of ItrEXPs in the SR development of I. trifida . The gene expression profiling in Y22 SR development revealed that ItrEXPAs and ItrEXLBs were down-regulated, and ItrEXPBs were up-regulated while ItrEXLAs were not obviously changed during the critical period of SR expansion, and might be beneficial to SR development. Combining the tissue-specific expression in young SR transverse sections of Y22 and sweetpotato tissue, we deduced that ItrEXLB05 , ItrEXLB07 and ItrEXLB08 might be the key genes for initial SR formation and enlargement, and ItrEXLA02 might be the key gene for root growth and development. This work provides new insights into the functions of the expansin gene family members in I. trifida , especially for EXLA and EXLB subfamilies genes in SR development.

MicroRNAs (miRNAs) play important roles in plant response to Cd stress. In our previous study, we observed significant differences in the expression levels of IamiR-4-3p between high-Cd and low-Cd cultivars of water spinach. The function of IamiR-4-3p was investigated by using wild type Arabidopsis (WT), Arabidopsis transfected with empty vector pCambia1302 (CK), and Arabidopsis transfected with IamiR-4-3p + vector pCambia1302 (p35S::miR-4-3p) in this study. In p35S::miR-4-3p Arabidopsis, the expression levels of GST3 and AWPM19-like were reduced by 20% and 24%. Under Cd treatment, higher root and shoot Cd concentrations were detected in the transgenic p35S::miR-4-3p Arabidopsis. MDA and H 2 O 2 concentrations were positively correlated with the Cd concentrations in all Arabidopsis. The elevated GSH pool in p35S::miR-4-3p Arabidopsis should compensate for its restricted GST3 expression in response to Cd-induced oxidative stress. Lower F1 (cell wall) and higher F2 (organelle) and F3 (soluble fraction) Cd concentrations were observed along with the reduced ABA level in p35S::miR-4-3p Arabidopsis, which could induce a weakened apoplastic barrier and higher Cd accumulation and translocation in roots. It is suggested that IamiR-4-3p is able to reduce the expression levels of GST3 and AWPM19-like, resulting in higher Cd uptake and translocation in Arabidopsis., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Cultivated sweetpotato [ Ipomoea batatas (L.) Lam.] from the family Convolvulaceae is a hexaploid species with 2 n = 6 x = 90 and has been controversial regarding its nature as an autopolyploid arising within a species or an allopolyploid forming between species. Here, we developed oligonucleotide-based painting probes for two chromosomes of I. nil , a model diploid Ipomoea species. Using these probes, we revealed the pairing behavior of homoeologous chromosomes in I. batatas and its two possible polyploid ancestral species, tetraploid I. tabascana (2 n = 4 x = 60) and hexaploid I. trifida (2 n = 6 x = 90). Chromosome painting analysis revealed a high percentage of quadrivalent formation in zygotene-pachytene cells of I. tabascana , which supported that I. tabascana was an autotetraploid likely derived by doubling of structurally similar and homologous genomes rather than a hybrid between I. batatas and I. trifida (2 x ). A high frequency of hexavalent/bivalent and tetravalent pairing was observed in I. trifida (6 x ) and I. batatas . However, the percentage of hexavalent pairing in I. trifida (6 x ) was far higher than that in I. batatas . Thus, the present results tend to support that I. trifida (6 x ) is an autohexaploid, while I. batatas is more likely to be a segmental allohexaploid.

Ipomea purpurea (L.) Roth. reduces dry land crop yield and quality in Northeast China, especially in Liaoning Province. Frequent use of thifensulfuron-methyl in recent years has resulted in herbicide resistance in I. purpurea. We evaluated resistance levels of I. purpurea to thifensulfuron-methyl, an acetolactate synthase (ALS) inhibitor, in Liaoning Province and further investigated the resistance mechanisms. The results showed that 15 populations of I. purpurea have evolved up to 5.81-34.44-fold resistance to thifensulfuron-methyl, compared to the susceptible population (S), among which LN3 was the most resistant. DNA sequencing of the ALS gene in susceptible and resistant populations did not reveal any target site mutations that could be associated with resistance to thifensulfuron-methyl in I. purpurea. Additionally, no significant difference was detected between the in vitro ALS activity of LN3 and S. The GR 50 of LN3 decreased sharply by 47% when malathion (a P450 inhibitor) was applied with thifensulfuron-methyl. Absorption of thifensulfuron-methyl by LN3 was equal to that of S; however, LN3 metabolized the herbicide significantly faster. This was repressed after the inhibition of P450s activity. Collectively, our results confirmed that I. purpurea in Liaoning Province has developed resistance to thifensulfuron-methyl and implied that the resistance was conferred by the increase in detoxification mediated by P450s. Furthermore, LN3 was sensitive to fluroxypyr, which can be used as an alternative to control I. purpurea., (Copyright © 2022 Elsevier Inc. All rights reserved.)

The origin of sweetpotato, a hexaploid species, is poorly understood, partly because the identity of its tetraploid progenitor remains unknown. In this study, we identify, describe and characterize a new species of Ipomoea that is sweetpotato's closest tetraploid relative known to date and probably a direct descendant of its tetraploid progenitor. We integrate morphological, phylogenetic, and genomic analyses of herbarium and germplasm accessions of the hexaploid sweetpotato, its closest known diploid relative Ipomoea trifida, and various tetraploid plants closely related to them from across the American continent. We identify wild autotetraploid plants from Ecuador that are morphologically distinct from Ipomoea batatas and I. trifida, but monophyletic and sister to I. batatas in phylogenetic analysis of nuclear data. We describe this new species as Ipomoea aequatoriensis T. Wells & P. Muñoz sp. nov., distinguish it from hybrid tetraploid material collected in Mexico; and show that it likely played a direct role in the origin of sweetpotato's hexaploid genome. This discovery transforms our understanding of sweetpotato's origin., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)

Ipomoea is a large pantropical genus globally distributed, which importance goes beyond the economic value as food resources or ornamental crops. This highly diverse genus has been the focus of a great number of studies, enriching the plant genomics knowledge, and challenging the plant evolution models. In the Carajás mountain range, located in Eastern Amazon, the savannah-like ferruginous ecosystem known as canga harbors highly specialized plant and animal populations, and Ipomoea is substantially representative in such restrictive habitat. Thus, to provide genetic data and insights into whole plastome phylogenetic relationships among key Ipomoea species from Eastern Amazon with little to none previously available data, we present the complete plastome sequences of twelve lineages of the genus, including the canga microendemic I. cavalcantei, the closely related I. marabaensis, and their putative hybrids. The twelve plastomes presented similar gene content as most publicly available Ipomoea plastomes, although the putative hybrids were correctly placed as closely related to the two parental species. The cavalcantei-marabaensis group was consistently grouped between phylogenetic methods. The closer relationship of the I. carnea plastome with the cavalcantei-marabaensis group, as well as the branch formed by I. quamoclit, I. asarifolia and I. maurandioides, were probably a consequence of insufficient taxonomic representativity, instead of true genetic closeness, reinforcing the importance of new plastome assemblies to resolve inconsistencies and boost statistical confidence, especially the case for South American clades of Ipomoea. The search for k-mers presenting high dispersion among the frequency distributions pointed to highly variable coding and intergenic regions, which may potentially contribute to the genetic diversity observed at species level. Our results contribute to the resolution of uncertain clades within Ipomoea and future phylogenomic studies, bringing unprecedented results to Ipomoea species with restricted distribution, such as I. cavalcantei., Competing Interests: The authors have declared that no competing interests exist.

Calcium-dependent protein kinase (CDPKs) is one of the calcium-sensing proteins in plants. They are likely to play important roles in growth and development and abiotic stress responses. However, these functions have not been explored in sweet potato. In this study, we identified 39 CDPK s in cultivated hexaploid sweet potato ( Ipomoea batatas , 2n = 6x = 90), 35 CDPKs in diploid relative Ipomoea trifida (2n = 2x = 30), and 35 CDPKs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological property, chromosome localization, phylogenetic relationship, gene structure, promoter cis -acting regulatory elements, and protein interaction network were systematically investigated to explore the possible roles of homologous CDPKs in the growth and development and abiotic stress responses of sweet potato. The expression profiles of the identified CDPKs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting the difference in the evolutionary trajectories of hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato CDPK genes and provide more candidate genes for improving yield and abiotic stress tolerance in cultivated sweet potato.

Although the evolution of the selfing syndrome often involves reductions in floral size, pollen and nectar, few studies of selfing syndrome divergence have examined nectar. We investigate whether nectar traits have evolved independently of other floral size traits in the selfing syndrome, whether nectar traits diverged due to drift or selection, and the extent to which quantitative trait locus (QTL) analyses predict genetic correlations. We use F5 recombinant inbred lines (RILs) generated from a cross between Ipomoea cordatotriloba and Ipomoea lacunosa. We calculate genetic correlations to identify evolutionary modules, test whether trait divergence was due to selection, identify QTLs and perform correlation analyses to evaluate how well QTL properties reflect genetic correlations. Nectar and floral size traits form separate evolutionary modules. Selection has acted to reduce nectar traits in the selfing I. lacunosa. Genetic correlations predicted from QTL properties are consistent with observed genetic correlations. Changes in floral traits associated with the selfing syndrome reflect independent evolution of at least two evolutionary modules: nectar and floral size traits. We also demonstrate directional selection on nectar traits, which is likely to be independent of selection on floral size traits. Our study also supports the expected mechanistic link between QTL properties and genetic correlations., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)

Premise: Darwin proposed that self-pollination in allegedly outcrossing species might act as a reproductive assurance mechanism when pollinators or mates are scarce; however, in natural populations, the benefits of selfing may be opposed by seed discounting and inbreeding depression. While empirical studies show variation among species and populations in the magnitude of reproductive assurance, little is known about the counterbalancing effects of inbreeding depression., Methods: By comparing the female reproductive success of emasculated and open-pollinated flowers, we assessed the reproductive assurance hypothesis in two Mexican populations of Ipomoea hederacea. In one population, we assessed temporal variation in reproductive assurance for three years. We evaluated inbreeding depression on seed production, seedling germination, and dry plant mass by contrasting self- and cross-hand pollination treatments in one population for two years., Result: The contribution of self-pollination to female reproductive success was high and consistent between populations, but there was variation in reproductive assurance across years. Inbreeding depression was absent in the early stages of progeny development, but there was a small negative effect of inbreeding in the probability of germination and the mass of adult progeny., Conclusions: Self-pollination provided significant reproductive assurance in I. hederacea but this contribution was variable across time. The contribution of reproductive assurance is probably reduced by inbreeding depression in later stages of progeny development, but this counter effect was small in the study populations. This study supports the hypothesis that reproductive assurance with limited inbreeding depression is likely an important selective force in the evolution of self-pollination in the genus Ipomoea., (© 2021 Botanical Society of America.)

Premise: Highly selfing plant species frequently display a distinctive suite of traits termed the selfing syndrome. Here we tested the hypothesis that these traits are grouped into correlated evolutionary modules and determined the degree of independence between such modules., Methods: We evaluated phenotypic correlations and QTL overlaps in F2 offspring of a cross between the morning glories Ipomoea lacunosa and I. cordatotriloba and investigated how traits clustered into modules at both the phenotypic and genetic level. We then compared our findings to other QTL studies of the selfing syndrome., Results: In the I. lacunosa selfing syndrome, traits grouped into modules that displayed correlated evolution within but not between modules. QTL overlap predicted phenotypic correlations, and QTLs affecting the same trait module were significantly physically clustered in the genome. The genetic architecture of the selfing syndrome varied across systems, but the pattern of stronger within- than between-module correlation was widespread., Conclusions: The genetic architecture we observe in the selfing syndrome is consistent with a growing understanding of floral morphological integration achieved via pleiotropy in clustered traits. This view of floral evolution is consistent with resource limitation or predation driving the evolution of the selfing syndrome, but invites further research into both the selective causes of the selfing syndrome and how genetic architecture itself evolves in response to changes in mating system., (© 2021 Botanical Society of America.)

Background: Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato., Results: The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages., Conclusions: Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

Wild relatives of crops are often rich in genetic resources and provide great possibilities for crop improvement. Ipomoea pes-caprae is one of the wild relatives of sweet potato and has high salt tolerance. Transcriptomes in the treatment and control groups at various times were sequenced to identify salt tolerance genes and salt response pathways. A total of 40,525 genes were obtained, of which 2478 and 3334 were differentially expressed in the roots and leaves of I. pes-caprae under salt stress, respectively. Identification of candidate genes revealed that the mitogen-activated protein kinase (MAPK) signaling pathway of plants and plant hormone signal transduction participates in the salt signal of I. pes-caprae under salt stress. Homology to ABI2 (HAB2) and Clade A protein phosphatases type 2C (HAI1), which encode two protein phosphatases 2C (PP2C) in the abscisic acid (ABA) signal pathway, were continuously up-regulated upon salt stress, indicating their key role in the salt signal transduction pathway of I. pes-caprae. The expression of EIN3-binding F-box protein 1 (EBF1) in the ethylene signaling pathway was also up-regulated, revealing that the salt tolerance of I. pes-caprae was related to the scavenging of reactive oxygen species (ROS). This study provides insights into the mechanism of salt-tolerant plants and the mining of salt-tolerant genes in sweet potato for the innovation of germplasm resources., (Copyright © 2020. Published by Elsevier GmbH.)

Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.

Phytochelatin synthases (PCSs) play a crucial part in heavy metal tolerance in plants via the synthesis of phytochelatins (PCs), which can chelate heavy metals (HMs) in the vacuole and decrease cell damage. Plant PCSs are commonly designated as key genes for phytoremediation. In this study, we identified a PCS gene (IpPCS1) from Ipomoea pes-caprae and investigated its role in regulating cadmium (Cd) tolerance and accumulation. The expression of a truncated IpPCS1t in yeast could complement the Cd-sensitive phenotype of the ycf1Δ mutant strain, as well as improve the Cd tolerance of the wild-type yeast strain, while promoting Cd accumulation in the yeast cells. The expression of IpPCS1 was induced in I. pes-caprae plants under Cd treatment. Compared with IpPCS1, the lack of a C-terminal in IpPCS1t did not affect its Cd tolerance, but might restrict the zinc (Zn) detoxification in yeast. The overexpression of IpPCS1t in Arabidopsis could improve the Cd tolerance slightly and had little impact on Cd accumulation in transgenic plant. Our results indicated that IpPCS1 has certain potential application value in Cd tolerance and detoxification, therefore provides a useful genetic resource for enhancing Cd tolerance and improving the Cd phytoremediation capacity of plants or organisms. In addition, our research is the first time to discover a new possible Cd activation site in the C-terminal of IpPCS1., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)

A quick, simple, and high-yield nucleic acid isolation process is crucial for high-quality DNA analysis. The ability of the MicroGEM PDQeX phytoGEM system and Omega Bio-tek E.Z.N.A.® Plant DS Mini kit to extract PCR-ready DNA was evaluated by extracting the forensically relevant "legal high" plant species: Ipomoea purpurea, Artemisia absinthium, Mitragyna speciosa, Datura stramonium, and Papaver somniferum. The plant material was pulverized, processed using the manufacturer's plant protocol for the PDQeX Nucleic Acid Extraction or the manufacturer's protocol for the Omega extraction, quantified using the Invitrogen Qubit 2.0 Fluorometer, and analyzed for amplifiability by PCR using a Qiagen Rotor-Gene Q instrument and published assays. The DNA amplicons for the legal high species produced high-resolution melt curves concordant with the melts observed when DNA was isolated using the Qiagen DNeasy Plant Mini Kit in previous studies., (© 2020 American Academy of Forensic Sciences.)

Molecular phylogenies are used as a basis for making inferences about macroevolutionary history. However, a robust phylogeny does not contain the information that is necessary to make many of these inferences. Complex methodologies that incorporate important assumptions about the nature of evolutionary history are therefore required. Here, we explore the implications of these assumptions for making inferences about the macroevolutionary history of Ipomoea - a large pantropical genus of flowering plants that contains the sweet potato (Ipomoea batatas), a crop of global economic importance. We focus on assumptions that underlie inferences of divergence times, and diversification parameters (speciation rates, extinction rates, and net diversification rates). These are among the most fundamental variables in macroevolutionary research. We use a series of novel approaches to explore the implications of these assumptions for inferring the age of Ipomoea, the ages of major clades within Ipomoea, whether there are significant differences in diversification parameters among clades within Ipomoea, and whether the storage root of I. batatas evolved in pre-human times. We show that inferring an age estimate for Ipomoea and major clades within Ipomoea is highly problematic. Inferred divergence times are sensitive to uncertain fossil calibrations and differing assumptions about among-branch-substitution-rate-variation. Despite this uncertainty, we are able to make robust inferences about patterns of variation in diversification parameters within Ipomoea, and that the storage root of I. batatas evolved in pre-human times. Taken together, this study presents novel and generalizable insights into the implications of methodological assumptions for making inferences about macroevolutionary history. Further, by presenting novel findings relating to the temporal dynamics of evolution in Ipomoea, as well as more specifically to I. batatas, this study makes a valuable contribution to our understanding of tropical plant evolution, and the evolutionary context in which economically important crops evolve., (Crown Copyright © 2020. Published by Elsevier Inc. All rights reserved.)

A common evolutionary trend in highly selfing plants is the evolution of the "selfing syndrome", in which traits associated with pollinator attraction are lost or greatly reduced. Limited information is available on whether these trait reductions are favored by natural selection or result from reduced purifying selection coupled with genetic drift. This study attempted to distinguish between these two possibilities for the evolutionary loss of floral pigmentation in the highly selfing species Ipomoea lacunosa. This study also tested the hypothesis that loss of floral pigmentation is caused by downregulation or loss of function in a tissue-specific anthocyanin transcription factor, as has been found in other plants. F2 individuals of a cross between white and pigmented individuals revealed segregation at two epistatically acting loci: one affecting pigmentation in both corolla throat and limbs (Anl1) and one affecting limb pigmentation (Anl2). Individuals that are homozygous for the "white" allele at Anl1 have white throats and limbs regardless of genotype at Anl2. In individuals with pigmented throats, homozygosity of the "white" allele at Anl2 produces white limbs. Flower color variation at Anl1 cosegregates with an R2R3-Myb anthocyanin transcription factor, which is down-regulated in white-flowers but not in pigmented flowers. Differential expression of the two alleles of this gene indicates that down regulation is caused by a cis-regulatory change. Finally, allele-frequency differences at Anl1 were substantially and significantly greater than differences in allele frequencies at four microsatellite loci. These results are consistent with the hypotheses that the identified R2R3-Myb gene corresponds to Anl1 and that evolutionary loss of pigmentation in I. lacunosa was caused by selection. They are also consistent with previous studies demonstrating that loss of floral pigmentation is usually caused by down-regulation or functional inactivation of an R2R3-Myb gene., Competing Interests: The authors have declared that no competing interests exist.

Although root traits play a critical role in mediating plant-plant interactions and resource acquisition from the soil environment, research examining whether and how belowground competition can influence the evolution of root traits remains largely unexplored. Here we examine the possibility that root traits may evolve as a target of selection from interspecific competition using Ipomoea purpurea and I. hederacea , two closely related morning glory species that commonly co-occur in the United States, as a model system. We show that belowground competitive interactions between the two species can alter the pattern of selection on root traits in each species. Specifically, competition with I. purpurea changes the pattern of selection on root angle in I. hederacea , and competitive interactions with I. hederacea change the pattern of selection on root size in I. purpurea . However, we did not uncover evidence that intraspecific competition altered the pattern of selection on any root traits within I. hederacea . Overall, our results suggest that belowground competition between closely related species can influence the phenotypic evolution of root traits in natural populations. Our findings provide a microevolutionary perspective of how competitive belowground interactions may impact plant fitness, potentially leading to patterns of plant community structure.

Background: DEAD-box protein family is the largest subfamily of RNA helicases and plays an important role in RNA metabolism and plant growth, development, and stress responses. Although DEAD-box genes have been characterized in various major crop plants, their identification and characterization in Convolvulaceae is still in infancy. Sweet potato (Ipomoea batatas, in Convolvulaceae) is the seventh most important crop in the world. Ipomoea trifida is one of the ancestors of sweet potato and is an effective resource for sweet potato cross-breeding., Objective: Identification and characterisation of DEAD-box transcription factors in sweet potato wild ancestor I. trifida genome., Method: A systematic genome-wide analysis was conducted to identify the DEAD-box transcription factors in the I. trifida genome., Results: We identified 17 ItfDEAD-box genes which distributed unevenly on the nine chromosomes of I. trifida and encoded 29 DEAD transcripts. The phylogenetic analysis classified the DEAD-box proteins into nine groups named I-IX. Homology model prediction of ItfDEAD-box proteins obtained 14 models which lay a preliminary foundation for the further functional exploration of the ItfDEAD-box proteins. The tissue-specific and abiotic stress-responsive expression profiles of ItfDEAD-box genes were analyzed in different tissues and under abiotic stress responses by RNA-seq data and confirmed by quantitative PCR analysis. Some genes were significantly up- or down-regulated by different abiotic stress, suggesting that ItfDEAD-box plays a crucial role in stress responses in I. trifida., Conclusion: The identification and gene expression of the ItfDEAD-box gene family might shed light on the function exploration of DEAD-box gene in I. trifida and promote the molecular breeding of sweet potato.

Ipomoea cairica is a tropical plant and a wild relative of the food plant sweet potato ( Ipomoea batatas ), listed as one of the most invasive alien species in China. Recently, it has been reported that I. cairica had successfully invaded mangrove wetlands, indicating its high salt tolerance. Based on previous genetic studies, I. cairica offers a good model for characterizing stress-resistant genes. It has recently been identified that the SRO proteins (SIMILAR TO RCD-ONE) play important roles in a variety of stress and developmental responses. Radical-Induced Cell Death1 (RCD1) was the first identified plant SRO protein from Arabidopsis thaliana . As a typical SRO protein, IcSRO1 had a highly conservative WWE domain, a conserved PARP fold and protein C in the RST function area. The expression of IcSRO1 was induced by salt, drought, and the plant hormone ABA. The transgenic Arabidopsis overexpressing IcSRO1 showed higher tolerance against salt and drought stress along with lower accumulation of hydrogen peroxide (H 2 O 2 ) and superoxide (O 2 - ) than the wild type. The IcSRO1 protein was localized in the nucleus after cultivation in the buffer. Our results indicated it could interact with Arabidopsis SALT OVERLY SENSITIVE 1 (AtSOS1), suggesting IcSRO1 may have similar functions. The pleiotropic effect of IcSRO1 on physiological processes contributes to the improvement of plant tolerance against diverse abiotic stresses, and may be associated with the adaptation of I. cairica to those environments with extreme saline and drought conditions. It therefore provides valuable gene resources for crop breeding enhancement.

The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci., Competing Interests: The authors have declared that no competing interests exist.

Background: GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China. However, the function of sweet potato GRAS genes remains unknown., Results: In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses., Conclusions: Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.

Late embryogenesis abundant (LEA) proteins belong to a large family that exists widely in plants and is mainly involved in desiccation processes during plant development or in the response to abiotic stresses. Here, we reported on an atypical LEA gene (IpLEA) related to salt tolerance from Ipomoea pes-caprae L. (Convolvulaceae). Sequence analysis revealed that IpLEA belongs to the LEA_2 (PF03168) group. IpLEA was shown to have a cytoplasmic localization pattern. Quantitative reverse transcription PCR analysis showed that IpLEA was widely expressed in different organs of the I. pes-caprae plants, and the expression levels increased following salt, osmotic, oxidative, freezing, and abscisic acid treatments. Analysis of the 1,495 bp promoter of IpLEA identified distinct cis-acting regulatory elements involved in abiotic stress. Induction of IpLEA improved Escherichia coli growth performance compared with the control under abiotic stresses. To further assess the function of IpLEA in plants, transgenic Arabidopsis plants overexpressing IpLEA were generated. The IpLEA-overexpressing Arabidopsis seedlings and adult plants showed higher tolerance to salt and drought stress than the wild-type. The transgenic plants also showed higher oxidative stress tolerance than the wild-type Arabidopsis. Furthermore, the expression patterns of a series of stress-responsive genes were affected. The results indicate that IpLEA is involved in the plant response to salt and drought, probably by mediating water homeostasis or by acting as a reactive oxygen species scavenger, thereby influencing physiological processes under various abiotic stresses in microorganisms and plants.